Table of Contents

• Spectral Clustering Gene Ontology Terms to Group Genes by FunctionNora Speer, Christian Spieth, Andreas Zell. 1-12 [doi]
• Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by ExpressionChaya Ben-Zaken Zilberstein, Michal Ziv-Ukelson. 13-26 [doi]
• Clustering Gene Expression Series with Prior KnowledgeLaurent Bréhélin. 27-38 [doi]
• A Linear Time Biclustering Algorithm for Time Series Gene Expression DataSara C. Madeira, Arlindo L. Oliveira. 39-52 [doi]
• Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic BackgroundsTamir Tuller, Efrat Oron, Erez Makavy, Daniel A. Chamovitz, Benny Chor. 53-64 [doi]
• A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency ProblemGang Wu, Jia-Huai You, Guohui Lin. 65-76 [doi]
• Computing the Quartet Distance Between Trees of Arbitrary DegreeChris Christiansen, Thomas Mailund, Christian N. S. Pedersen, Martin Randers. 77-88 [doi]
• Using Semi-definite Programming to Enhance Supertree ResolvabilityShlomo Moran, Satish Rao, Sagi Snir. 89-103 [doi]
• An Efficient Reduction from Constrained to Unconstrained Maximum Agreement SubtreeZ. S. Peng, H. F. Ting. 104-115 [doi]
• Pattern Identification in BiogeographyGaneshkumar Ganapathy, Barbara Goodson, Robert K. Jansen, Vijaya Ramachandran, Tandy Warnow. 116-127 [doi]
• On the Complexity of Several Haplotyping ProblemsRudi Cilibrasi, Leo van Iersel, Steven Kelk, John Tromp. 128-139 [doi]
• A Hidden Markov Technique for Haplotype ReconstructionPasi Rastas, Mikko Koivisto, Heikki Mannila, Esko Ukkonen. 140-151 [doi]
• Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination EventYun S. Song, Yufeng Wu, Dan Gusfield. 152-164 [doi]
• A Faster Algorithm for Detecting Network MotifsSebastian Wernicke. 165-177 [doi]
• Reaction Motifs in Metabolic NetworksVincent Lacroix, Cristina G. Fernandes, Marie-France Sagot. 178-191 [doi]
• Reconstructing Metabolic Networks Using Interval AnalysisWarwick Tucker, Vincent Moulton. 192-203 [doi]
• A 1.375-Approximation Algorithm for Sorting by TranspositionsIsaac Elias, Tzvika Hartman. 204-215 [doi]
• A New Tight Upper Bound on the Transposition DistanceAnthony Labarre. 216-227 [doi]
• Perfect Sorting by Reversals Is Not Always DifficultSèverine Bérard, Anne Bergeron, Cedric Chauve, Christophe Paul. 228-238 [doi]
• Minimum Recombination Histories by Branch and BoundRune B. Lyngsø, Yun S. Song, Jotun Hein. 239-250 [doi]
• A Unifying Framework for Seed Sensitivity and Its Application to Subset SeedsGregory Kucherov, Laurent Noé, Mikhail A. Roytberg. 251-263 [doi]
• Generalized Planted (::::l::::, ::::d::::)-Motif Problem with Negative SetHenry C. M. Leung, Francis Y. L. Chin. 264-275 [doi]
• Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens Stoye. 276-290 [doi]
• The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence SimilarityDaniel Dalevi, Devdatt P. Dubhashi. 291-302 [doi]
• Multiple Structural RNA Alignment with Lagrangian RelaxationMarkus Bauer, Gunnar W. Klau, Knut Reinert. 303-314 [doi]
• Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise ComparisonsPankaj K. Agarwal, Yonatan Bilu, Rachel Kolodny. 315-327 [doi]
• Ortholog Clustering on a Multipartite GraphAkshay Vashist, Casimir A. Kulikowski, Ilya B. Muchnik. 328-340 [doi]
• Linear Time Algorithm for Parsing RNA Secondary StructureBaharak Rastegari, Anne Condon. 341-352 [doi]
• A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus PerformanceRobert S. Boyer, Warren A. Hunt Jr., Serita M. Nelesen. 353-364 [doi]
• Optimal Protein Threading by Cost-SplittingPhilippe Veber, Nicola Yanev, Rumen Andonov, Vincent Poirriez. 365-375 [doi]
• Efficient Parameterized Algorithm for Biopolymer Structure-Sequence AlignmentYinglei Song, Chunmei Liu, Xiuzhen Huang, Russell L. Malmberg, Ying Xu, Liming Cai. 376-388 [doi]
• Rotamer-Pair Energy Calculations Using a Trie Data StructureAndrew Leaver-Fay, Brian Kuhlman, Jack Snoeyink. 389-400 [doi]
• Improved Maintenance of Molecular Surfaces Using Dynamic Graph ConnectivityEran Eyal, Dan Halperin. 401-413 [doi]
• The Main Structural Regularities of the Sandwich ProteinsAlexander Kister. 414-422 [doi]
• Discovery of Protein Substructures in EM MapsKeren Lasker, Oranit Dror, Ruth Nussinov, Haim J. Wolfson. 423-434 [doi]